pninexus 3.2.2__tar.gz → 3.2.3__tar.gz

pninexus-3.2.3/PKG-INFO

@@ -0,0 +1,180 @@
+Metadata-Version: 2.1
+Name: pninexus
+Version: 3.2.3
+Summary: Python wrapper for the H5CPP and PNI libraries
+Home-page: https://github.com/pni-libraries/python-pninexus
+Author: Eugen Wintersberger
+Author-email: eugen.wintersberger@desy.de
+Maintainer: Eugen Wintersberger, Jan Kotanski
+Maintainer-email: jan.kotanski@desy.de
+License: GPLv2
+Keywords: h5cpp hdf5 python photon science detector
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+License-File: LICENSE
+
+Python bindings for PNI/NeXus and h5cpp
+=======================================
+
+
+|github workflow|
+|docs|
+|Pypi Version|
+|Python Versions|
+
+.. |github workflow| image:: https://github.com/pni-libraries/python-pninexus/actions/workflows/tests.yml/badge.svg
+   :target: https://github.com/pni-libraries/python-pninexus/actions
+   :alt:
+
+.. |docs| image:: https://img.shields.io/badge/Documentation-webpages-ADD8E6.svg
+   :target: https://pni-libraries.github.io/python-pninexus/index.html
+   :alt:
+
+.. |Pypi Version| image:: https://img.shields.io/pypi/v/pninexus.svg
+                  :target: https://pypi.python.org/pypi/pninexus
+                  :alt:
+
+.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/pninexus.svg
+                     :target: https://pypi.python.org/pypi/pninexus/
+                     :alt:
+
+
+Python wrapper for the `h5cpp <https://github.com/ess-dmsc/h5cpp>`__ and
+`libpninexus <https://github.com/pni-libraries/libpninexus>`__ C++
+libraries. The wrapper supports Python 2.X and 3.X.
+
+Installation
+------------
+
+Required packages
+~~~~~~~~~~~~~~~~~
+
+-  *h5cpp* >= 0.5.0
+-  *libpninexus* >= 3.2.0
+-  python setuptools
+-  numpy
+-  c++ compiler
+-  boost-python library
+-  python sphinx to build the documentation
+
+Install from sources
+~~~~~~~~~~~~~~~~~~~~
+
+The code can be built with
+
+::
+
+       $ python setup.py install
+
+For those who are still running on the old interface it is maybe whise
+to install this package in a custom location with something like this
+
+::
+
+       $ python setup.py install --prefix=<path to installation prefix>
+
+To build the documentation use
+
+::
+
+       $ python setup.py build_sphinx
+
+The resulting documentation can be found below ``build/sphinx/html`` in
+the root directory of the source distribution.
+
+Finally, the package can be tested using
+
+::
+
+       $ python setup.py test
+
+For Python3 just replace python with python3 in the above instructions.
+
+Debian and Ubuntu packages
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Debian ``bookworm``, ``bullseye``, ``buster`` or Ubuntu ``oracular``,
+``noble``, ``jammy`` packages can be found in the HDRI repository.
+
+To install the debian packages, add the PGP repository key
+
+::
+
+       $ sudo su
+       $ curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
+       $ chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
+
+and then download the corresponding source list, e.g. for ``bookworm``
+
+::
+
+       $ cd /etc/apt/sources.list.d
+       $ wget http://repos.pni-hdri.de/bookworm-pni-hdri.list
+
+or ``noble``
+
+::
+
+       $ cd /etc/apt/sources.list.d
+       $ wget http://repos.pni-hdri.de/noble-pni-hdri.list
+
+respectively.
+
+Finally,
+
+::
+
+       $ apt-get update
+       $ apt-get install python3-pninexus
+
+or
+
+::
+
+       $ apt-get update
+       $ apt-get install python-pninexus
+
+for python2.
+
+
+Manylinux wheels from PyPI
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To install pninexus in a conda or python virtual environment manylinux pip wheels can be used, e.g.
+
+.. code-block:: console
+
+   $ python3 -m venv myvenv
+   $ . myvenv/bin/activate
+   
+   $ pip install pip --upgrade
+   $ pip install numpy
+   
+   $ pip install pninexus -U wheel
+
+For some versions of wheels numpy needs to be installed in advance.
+
+Starting from v3.2.2 the pninexus wheel contains the most important external filters.
+In order to use them one needs to set HDF5_PLUGIN_PATH e.g. by
+
+.. code-block:: python
+
+   import pninexus
+
+
+More information can be found at `online
+documentation <https://pni-libraries.github.io/python-pninexus/index.html>`__.
+
+Changes for a specific version of libpninexus can be found at
+`CHANGELOG <https://github.com/pni-libraries/python-pninexus/blob/develop/CHANGELOG.md>`__.
+

{pninexus-3.2.2 → pninexus-3.2.3}/README.rst

@@ -78,8 +78,8 @@ For Python3 just replace python with python3 in the above instructions.
 Debian and Ubuntu packages
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Debian ``bookworm``, ``bullseye``, ``buster`` or Ubuntu ``lunar``,
-``jammy``, ``focal`` packages can be found in the HDRI repository.
+Debian ``bookworm``, ``bullseye``, ``buster`` or Ubuntu ``oracular``,
+``noble``, ``jammy`` packages can be found in the HDRI repository.
 
 To install the debian packages, add the PGP repository key
 
@@ -89,19 +89,19 @@ To install the debian packages, add the PGP repository key
        $ curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
        $ chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
 
-and then download the corresponding source list, e.g. for ``bullseye``
+and then download the corresponding source list, e.g. for ``bookworm``
 
 ::
 
        $ cd /etc/apt/sources.list.d
-       $ wget http://repos.pni-hdri.de/bullseye-pni-hdri.list
+       $ wget http://repos.pni-hdri.de/bookworm-pni-hdri.list
 
-or ``jammy``
+or ``noble``
 
 ::
 
        $ cd /etc/apt/sources.list.d
-       $ wget http://repos.pni-hdri.de/jammy-pni-hdri.list
+       $ wget http://repos.pni-hdri.de/noble-pni-hdri.list
 
 respectively.
 
@@ -110,16 +110,16 @@ Finally,
 ::
 
        $ apt-get update
-       $ apt-get install python-pninexus
+       $ apt-get install python3-pninexus
 
 or
 
 ::
 
        $ apt-get update
-       $ apt-get install python3-pninexus
+       $ apt-get install python-pninexus
 
-for python3.
+for python2.
 
 
 Manylinux wheels from PyPI

{pninexus-3.2.2 → pninexus-3.2.3}/doc/sphinx/conf.py

@@ -160,7 +160,7 @@ html_sidebars = {
 
 html_context = {
     "docs_versions" : [
-        "v3.2.2", "v3.2.1", "v3.2.0", "v3.1.0",
+        "v3.2.3", "v3.2.2", "v3.2.1", "v3.2.0", "v3.1.0",
         "v3.0.3", "v3.0.2", "v3.0.1", "v3.0.0", "v2.0.0", "v1.3.4"]
 }
 

{pninexus-3.2.2 → pninexus-3.2.3}/doc/sphinx/h5cpp_datatypes.rst

@@ -110,4 +110,4 @@ the array. In terms of HDF5 that would be
 
    datatype = String.fixed(str_len)
    datatype.padding  = StringPad.NULLPAD
-   datatype.encoding = CharachterEncoding.UTF8
+   datatype.encoding = CharacterEncoding.UTF8

{pninexus-3.2.2 → pninexus-3.2.3}/setup.py

@@ -20,8 +20,8 @@ except ImportError:
     BuildDoc = None
 
 name = "pninexus"
-version = "3.2.2"
-release = "3.2.2"
+version = "3.2.3"
+release = "3.2.3"
 # release = "3.2"
 
 if release.count(".") == 1:
@@ -278,6 +278,7 @@ setup(
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     test_suite="test",
     test_loader="unittest:TestLoader",

{pninexus-3.2.2 → pninexus-3.2.3}/src/cpp/nexus/element_dict_converter.cpp

@@ -92,7 +92,7 @@ void* dict_to_nxpath_element_converter::convertible(PyObject *obj_ptr)
 string get_string_from_pyobject(PyObject *ptr)
 {
 #if PY_MAJOR_VERSION >= 3
-    Py_ssize_t str_size = PyUnicode_GET_DATA_SIZE(ptr);
+    Py_ssize_t str_size = PyUnicode_GET_LENGTH(ptr);
     if(str_size)
     {
         PyObject *utf8_str = PyUnicode_AsUTF8String(ptr);

{pninexus-3.2.2 → pninexus-3.2.3}/src/pninexus/h5cpp/attribute/__init__.py

@@ -20,15 +20,28 @@ def attribute_write(self, data):
     write_data = data
     if not isinstance(write_data, numpy.ndarray):
         write_data = numpy.array(write_data)
-
     if write_data.dtype.kind == 'U':
-        write_data = write_data.astype("S")
+        try:
+            write_data = write_data.astype("S")
+        except Exception:
+            if isinstance(data, numpy.ndarray) and data.shape:
+                shape = data.shape
+                if len(shape) > 1:
+                    data = data.flatten()
+                write_data = numpy.array(
+                    [bytes(str(dt).encode('utf-8')) for dt in data])
+                if len(shape) > 1:
+                    write_data = write_data.reshape(shape)
+            else:
+                write_data = numpy.array(str(data).encode('utf-8'))
     elif write_data.dtype == 'bool':
         write_data = write_data.astype("int8")
 
+    #  print("DATA", data, write_data)
     try:
         self._write(write_data)
-    except RuntimeError:
+    except RuntimeError as e:
+        print(str(e))
         print(write_data, write_data.dtype)
 
 

{pninexus-3.2.2 → pninexus-3.2.3}/src/pninexus/h5cpp/node/__init__.py

@@ -275,8 +275,19 @@ def dataset_write(self, data, selection=None):
     # if the data is a unicode numpy array we have to convert it to a
     # simple string array
     if data.dtype.kind == 'U':
-        data = data.astype('S')
-
+        try:
+            data = data.astype('S')
+        except Exception:
+            if isinstance(data, numpy.ndarray) and data.shape:
+                shape = data.shape
+                if len(shape) > 1:
+                    data = data.flatten()
+                data = numpy.array(
+                    [bytes(str(dt).encode('utf-8')) for dt in data])
+                if len(shape) > 1:
+                    data = data.reshape(shape)
+            else:
+                data = numpy.array(str(data).encode('utf-8'))
     #
     # determine memory datatype and dataspace
     # - if the file type is a variable length string we have to adjust the

pninexus-3.2.3/src/pninexus.egg-info/PKG-INFO

@@ -0,0 +1,180 @@
+Metadata-Version: 2.1
+Name: pninexus
+Version: 3.2.3
+Summary: Python wrapper for the H5CPP and PNI libraries
+Home-page: https://github.com/pni-libraries/python-pninexus
+Author: Eugen Wintersberger
+Author-email: eugen.wintersberger@desy.de
+Maintainer: Eugen Wintersberger, Jan Kotanski
+Maintainer-email: jan.kotanski@desy.de
+License: GPLv2
+Keywords: h5cpp hdf5 python photon science detector
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+License-File: LICENSE
+
+Python bindings for PNI/NeXus and h5cpp
+=======================================
+
+
+|github workflow|
+|docs|
+|Pypi Version|
+|Python Versions|
+
+.. |github workflow| image:: https://github.com/pni-libraries/python-pninexus/actions/workflows/tests.yml/badge.svg
+   :target: https://github.com/pni-libraries/python-pninexus/actions
+   :alt:
+
+.. |docs| image:: https://img.shields.io/badge/Documentation-webpages-ADD8E6.svg
+   :target: https://pni-libraries.github.io/python-pninexus/index.html
+   :alt:
+
+.. |Pypi Version| image:: https://img.shields.io/pypi/v/pninexus.svg
+                  :target: https://pypi.python.org/pypi/pninexus
+                  :alt:
+
+.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/pninexus.svg
+                     :target: https://pypi.python.org/pypi/pninexus/
+                     :alt:
+
+
+Python wrapper for the `h5cpp <https://github.com/ess-dmsc/h5cpp>`__ and
+`libpninexus <https://github.com/pni-libraries/libpninexus>`__ C++
+libraries. The wrapper supports Python 2.X and 3.X.
+
+Installation
+------------
+
+Required packages
+~~~~~~~~~~~~~~~~~
+
+-  *h5cpp* >= 0.5.0
+-  *libpninexus* >= 3.2.0
+-  python setuptools
+-  numpy
+-  c++ compiler
+-  boost-python library
+-  python sphinx to build the documentation
+
+Install from sources
+~~~~~~~~~~~~~~~~~~~~
+
+The code can be built with
+
+::
+
+       $ python setup.py install
+
+For those who are still running on the old interface it is maybe whise
+to install this package in a custom location with something like this
+
+::
+
+       $ python setup.py install --prefix=<path to installation prefix>
+
+To build the documentation use
+
+::
+
+       $ python setup.py build_sphinx
+
+The resulting documentation can be found below ``build/sphinx/html`` in
+the root directory of the source distribution.
+
+Finally, the package can be tested using
+
+::
+
+       $ python setup.py test
+
+For Python3 just replace python with python3 in the above instructions.
+
+Debian and Ubuntu packages
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Debian ``bookworm``, ``bullseye``, ``buster`` or Ubuntu ``oracular``,
+``noble``, ``jammy`` packages can be found in the HDRI repository.
+
+To install the debian packages, add the PGP repository key
+
+::
+
+       $ sudo su
+       $ curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
+       $ chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
+
+and then download the corresponding source list, e.g. for ``bookworm``
+
+::
+
+       $ cd /etc/apt/sources.list.d
+       $ wget http://repos.pni-hdri.de/bookworm-pni-hdri.list
+
+or ``noble``
+
+::
+
+       $ cd /etc/apt/sources.list.d
+       $ wget http://repos.pni-hdri.de/noble-pni-hdri.list
+
+respectively.
+
+Finally,
+
+::
+
+       $ apt-get update
+       $ apt-get install python3-pninexus
+
+or
+
+::
+
+       $ apt-get update
+       $ apt-get install python-pninexus
+
+for python2.
+
+
+Manylinux wheels from PyPI
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To install pninexus in a conda or python virtual environment manylinux pip wheels can be used, e.g.
+
+.. code-block:: console
+
+   $ python3 -m venv myvenv
+   $ . myvenv/bin/activate
+   
+   $ pip install pip --upgrade
+   $ pip install numpy
+   
+   $ pip install pninexus -U wheel
+
+For some versions of wheels numpy needs to be installed in advance.
+
+Starting from v3.2.2 the pninexus wheel contains the most important external filters.
+In order to use them one needs to set HDF5_PLUGIN_PATH e.g. by
+
+.. code-block:: python
+
+   import pninexus
+
+
+More information can be found at `online
+documentation <https://pni-libraries.github.io/python-pninexus/index.html>`__.
+
+Changes for a specific version of libpninexus can be found at
+`CHANGELOG <https://github.com/pni-libraries/python-pninexus/blob/develop/CHANGELOG.md>`__.
+

{pninexus-3.2.2 → pninexus-3.2.3}/src/pninexus.egg-info/SOURCES.txt

@@ -99,6 +99,14 @@ src/pninexus.egg-info/dependency_links.txt
 src/pninexus.egg-info/requires.txt
 src/pninexus.egg-info/top_level.txt
 src/pninexus/filters/__init__.py
+src/pninexus/filters/libh5blosc.so
+src/pninexus/filters/libh5bshuf.so
+src/pninexus/filters/libh5bz2.so
+src/pninexus/filters/libh5jpeg.so
+src/pninexus/filters/libh5lz4.so
+src/pninexus/filters/libh5lzf.so
+src/pninexus/filters/libh5mafisc.so
+src/pninexus/filters/libh5zfp.so
 src/pninexus/h5cpp/__init__.py
 src/pninexus/h5cpp/attribute/__init__.py
 src/pninexus/h5cpp/dataspace/__init__.py

{pninexus-3.2.2 → pninexus-3.2.3}/test/h5cpp_tests/attribute_tests/attribute_io_test.py

@@ -118,7 +118,7 @@ class AttributeIOTests(unittest.TestCase):
         a = self.root.attributes.create("StringScalar", dtype)
         a.write("hello world")
         r = a.read()
-        self.assertEqual(r, "hello world")
+        self.assertEqual(r, data)
 
     def testStringScalarVariableLength(self):
 
@@ -128,6 +128,16 @@ class AttributeIOTests(unittest.TestCase):
         r = a.read()
         self.assertEqual(r, data)
 
+    def testStringUTF8ScalarVariableLength(self):
+
+        data = u"µm"
+        dtype = String.variable()
+        dtype.encoding = h5cpp.datatype.CharacterEncoding.UTF8
+        a = self.root.attributes.create("StringUTF8ScalarVLength", dtype)
+        a.write(data)
+        r = a.read()
+        self.assertEqual(r, data)
+
     def testStringArray(self):
 
         data = numpy.array([["hello", "world", "this"], ["is", "a", "test"]])
@@ -147,6 +157,17 @@ class AttributeIOTests(unittest.TestCase):
         r = a.read()
         npt.assert_array_equal(r, data)
 
+    def testStringUTF8ArrayVariableLength(self):
+
+        data = numpy.array([u"µm", u"µA"])
+        dtype = String.variable()
+        dtype.encoding = h5cpp.datatype.CharacterEncoding.UTF8
+        a = self.root.attributes.create(
+            "StringUTF8ArrayVLength", dtype, (2,))
+        a.write(data)
+        r = a.read()
+        npt.assert_array_equal(r, data)
+
     def testIntArray(self):
 
         data = numpy.array([1, 2, 3])

{pninexus-3.2.2 → pninexus-3.2.3}/test/h5cpp_tests/filter_tests/creation_test.py

@@ -229,7 +229,7 @@ class FilterCreationTest(unittest.TestCase):
                 filters[0].name,
                 "bitshuffle; see https://github.com/kiyo-masui/bitshuffle")
         else:
-            raise Exception("Bitshuffle filter is not available")
+            # raise Exception("Bitshuffle filter is not available")
             error = False
             try:
                 filter(self.dcpl)

{pninexus-3.2.2 → pninexus-3.2.3}/test/h5cpp_tests/node_tests/dataset_io_test.py

@@ -115,6 +115,17 @@ class DatasetAllIOTests(unittest.TestCase):
         read = dataset.read()
         self.assertEqual(read, "hello world")
 
+    def testWriteVariableLengthUTF8Scalar(self):
+        data = u"µm"
+        dtype = h5cpp.datatype.String.variable()
+        dtype.encoding = h5cpp.datatype.CharacterEncoding.UTF8
+        dataset = Dataset(
+            self.root, h5cpp.Path("VariableLengthStringUTF8Scalar"),
+            dtype, Scalar())
+        dataset.write(data)
+        read = dataset.read()
+        self.assertEqual(read, data)
+
     def testWriteIntegerArray(self):
 
         data = numpy.array([[1, 2, 3, 4], [5, 6, 7, 8]])
@@ -222,3 +233,17 @@ class DatasetAllIOTests(unittest.TestCase):
         dataset.write(data)
         read = dataset.read()
         npt.assert_array_equal(read, data)
+
+    def testWriteVariableLengthStringUTF8Array(self):
+
+        data = numpy.array([u"µm", u"µA"])
+        dtype = h5cpp.datatype.String.variable()
+        dtype.encoding = h5cpp.datatype.CharacterEncoding.UTF8
+        dataset = Dataset(
+            self.root,
+            h5cpp.Path("VariableLengthStringUTF8Array"),
+            dtype,
+            Simple((2,)))
+        dataset.write(data)
+        read = dataset.read()
+        npt.assert_array_equal(read, data)